EZH2 is a chromatin-modifying enzyme targeting histone proteins. Specifically, EZH2 protein is the catalytic subunit of Polycomb Repressive Complex 2 (PRC2), which is a histone methyltransferase specific for lysine-27 (K27) of histone 3 (H3). Methylated H3-K27 is associated with gene repression. Abnormally elevated levels of EZH2 have been found in various cancer tissues and are associated with gene repression, reviewed in Simon, J., and Lange, C. (2008) Roles of EZH2 histone methyltransferase in cancer epigenetics, Mut. Res. 647:21. It was also discovered that specific mutations alter the histone-modifying function of EZH2 protein by altering its substrate preference. EZH2 mutated at position Y646 (see Wiggle, T., et al. (2011) FEBS Lett. 585:3011) is abnormally active at methylating di-methylated H3 (H3K27me2) into the tri-methylated form (H3K27me3). EZH2 mutated at position A692 (see Majer, C., et al. (2012) FEBS Lett, 586:3348) is abnormally active at di-methylation; and EZH2 mutated at position A682 (see McCabe, M., et al. (2012), PNAS 109:2989) is abnormally active at all three methylation steps. In human cancer, these mutations have been shown to promote gene repression via histone hypermethylation.
Therapies targeting EZH2 have been developed. Selective small molecules inhibitors of EZH2 have been shown to block EZH2 (and PRC2) activity and promote killing of cancer cells in vitro. (Knutson, S, et al. (2012) Nature Chem. Bio. 8:890. The inhibitor is uniquely effective at killing cells with abnormally active mutant EZH2 without affecting cells with wild-type EZH2 (Id.) Therefore, a companion diagnostic test is necessary to identify patients whose tumors have mutant EZH2 and will likely benefit from the EZH2 inhibitors. It is essential that a clinical test for EZH2 mutations target as many mutations as possible with adequate sensitivity. This will assure that patients with rare mutations do not receive a “false negative” test result and miss out on a potentially life-saving treatment. At the same time, the test should be highly specific to ensure that patients do not receive a “false positive” result and receive costly and ineffective treatment.
One technique that is sensitive and amenable to multiplexing is allele-specific PCR (AS-PCR). This technique detects mutations or polymorphisms in nucleic acid sequences in the presence of wild-type variants of the sequences. In a successful allele-specific PCR, the desired variant of the target nucleic acid is amplified, while the other variants are not, at least not to a detectable level. In an allele-specific PCR, at least one primer is allele-specific such that primer extension occurs only when the specific variant of the sequence is present. One or more allele-specific primers targeting one or more polymorphic sites can be present in the same reaction mixture. Design of successful allele-specific primers is an unpredictable art. While it is routine to design a primer for a known sequence, no formula exists for designing a primer that can discriminate between very similar sequences.
In the context of a diagnostic assay, precise discrimination is required. For example, in the context of the EZH2 mutation detection, the performance of the allele-specific primer may determine the course of a patient's cancer therapy. Thus there is a need for a comprehensive assay capable of detecting a maximum number of EZH2 mutations with maximum specificity and sensitivity.